Re: AMBER: MD problems/shake

From: Bill Ross <>
Date: Mon, 19 Dec 2005 12:59:04 -0800 (PST)

> NITER, NIT, LL, I and J are : 0 1 2089 4153 4154
> If 4153 and 4154 are problematic atoms numer
> than this is a ligand problem, but it seems perfectly ok.

So the bond between these atoms has a large force on it..
if the atoms are in a new residue type that you created,
see what charges are on those atoms. Also see if one is
an H type with vdw radius = 0. Finally look at the atoms
around that area in case something else is somehow impinging
on that area.

This is assuming that you equilibrated carefully and got a
good trajectory after that and before this event.

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Received on Mon Dec 19 2005 - 21:53:01 PST
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